[{"_id":"15628","project":[{"_id":"52","name":"Computing Resources Provided by the Paderborn Center for Parallel Computing"}],"user_id":"40778","article_number":"201910208","language":[{"iso":"eng"}],"publication":"Proceedings of the National Academy of Sciences","type":"journal_article","abstract":[{"text":"<jats:p>The three-dimensional (3D) crystal structures of the GAF3 domain of cyanobacteriochrome Slr1393 (<jats:italic>Synechocystis</jats:italic> PCC6803) carrying a phycocyanobilin chromophore could be solved in both 15-<jats:italic>Z</jats:italic> dark-adapted state, Pr, λ<jats:sub>max</jats:sub> = 649 nm, and 15-<jats:italic>E</jats:italic> photoproduct, Pg, λ<jats:sub>max</jats:sub> = 536 nm (resolution, 1.6 and 1.86 Å, respectively). The structural data allowed identifying the large spectral shift of the Pr-to-Pg conversion as resulting from an out-of-plane rotation of the chromophore’s peripheral rings and an outward movement of a short helix formed from a formerly unstructured loop. In addition, a third structure (2.1-Å resolution) starting from the photoproduct crystals allowed identification of elements that regulate the absorption maxima. In this peculiar form, generated during X-ray exposition, protein and chromophore conformation still resemble the photoproduct state, except for the D-ring already in 15-<jats:italic>Z</jats:italic> configuration and tilted out of plane akin the dark state. Due to its formation from the photoproduct, it might be considered an early conformational change initiating the parental state-recovering photocycle. The high quality and the distinct features of the three forms allowed for applying quantum-chemical calculations in the framework of multiscale modeling to rationalize the absorption maxima changes. A systematic analysis of the PCB chromophore in the presence and absence of the protein environment showed that the direct electrostatic effect is negligible on the spectral tuning. However, the protein forces the outer pyrrole rings of the chromophore to deviate from coplanarity, which is identified as the dominating factor for the color regulation.</jats:p>","lang":"eng"}],"status":"public","date_updated":"2022-01-06T06:52:30Z","author":[{"full_name":"Xu, Xiuling","last_name":"Xu","first_name":"Xiuling"},{"last_name":"Port","full_name":"Port, Astrid","first_name":"Astrid"},{"last_name":"Wiebeler","full_name":"Wiebeler, Christian","first_name":"Christian"},{"full_name":"Zhao, Kai-Hong","last_name":"Zhao","first_name":"Kai-Hong"},{"first_name":"Igor","full_name":"Schapiro, Igor","last_name":"Schapiro"},{"first_name":"Wolfgang","full_name":"Gärtner, Wolfgang","last_name":"Gärtner"}],"date_created":"2020-01-23T08:16:24Z","title":"Structural Elements Regulating the Photochromicity in a Cyanobacteriochrome","doi":"10.1073/pnas.1910208117","publication_identifier":{"issn":["0027-8424","1091-6490"]},"publication_status":"published","year":"2020","citation":{"mla":"Xu, Xiuling, et al. “Structural Elements Regulating the Photochromicity in a Cyanobacteriochrome.” <i>Proceedings of the National Academy of Sciences</i>, 201910208, 2020, doi:<a href=\"https://doi.org/10.1073/pnas.1910208117\">10.1073/pnas.1910208117</a>.","short":"X. Xu, A. Port, C. Wiebeler, K.-H. Zhao, I. Schapiro, W. Gärtner, Proceedings of the National Academy of Sciences (2020).","bibtex":"@article{Xu_Port_Wiebeler_Zhao_Schapiro_Gärtner_2020, title={Structural Elements Regulating the Photochromicity in a Cyanobacteriochrome}, DOI={<a href=\"https://doi.org/10.1073/pnas.1910208117\">10.1073/pnas.1910208117</a>}, number={201910208}, journal={Proceedings of the National Academy of Sciences}, author={Xu, Xiuling and Port, Astrid and Wiebeler, Christian and Zhao, Kai-Hong and Schapiro, Igor and Gärtner, Wolfgang}, year={2020} }","apa":"Xu, X., Port, A., Wiebeler, C., Zhao, K.-H., Schapiro, I., &#38; Gärtner, W. (2020). Structural Elements Regulating the Photochromicity in a Cyanobacteriochrome. <i>Proceedings of the National Academy of Sciences</i>. <a href=\"https://doi.org/10.1073/pnas.1910208117\">https://doi.org/10.1073/pnas.1910208117</a>","chicago":"Xu, Xiuling, Astrid Port, Christian Wiebeler, Kai-Hong Zhao, Igor Schapiro, and Wolfgang Gärtner. “Structural Elements Regulating the Photochromicity in a Cyanobacteriochrome.” <i>Proceedings of the National Academy of Sciences</i>, 2020. <a href=\"https://doi.org/10.1073/pnas.1910208117\">https://doi.org/10.1073/pnas.1910208117</a>.","ieee":"X. Xu, A. Port, C. Wiebeler, K.-H. Zhao, I. Schapiro, and W. Gärtner, “Structural Elements Regulating the Photochromicity in a Cyanobacteriochrome,” <i>Proceedings of the National Academy of Sciences</i>, 2020.","ama":"Xu X, Port A, Wiebeler C, Zhao K-H, Schapiro I, Gärtner W. Structural Elements Regulating the Photochromicity in a Cyanobacteriochrome. <i>Proceedings of the National Academy of Sciences</i>. 2020. doi:<a href=\"https://doi.org/10.1073/pnas.1910208117\">10.1073/pnas.1910208117</a>"}},{"date_created":"2021-09-01T09:47:27Z","author":[{"first_name":"Julia","full_name":"Haddad, Julia","last_name":"Haddad"},{"first_name":"Diego","full_name":"Pontoni, Diego","last_name":"Pontoni"},{"full_name":"Murphy, Bridget M.","last_name":"Murphy","first_name":"Bridget M."},{"first_name":"Sven","full_name":"Festersen, Sven","last_name":"Festersen"},{"full_name":"Runge, Benjamin","last_name":"Runge","first_name":"Benjamin"},{"last_name":"Magnussen","full_name":"Magnussen, Olaf M.","first_name":"Olaf M."},{"id":"84268","full_name":"Steinrück, Hans-Georg","orcid":"0000-0001-6373-0877","last_name":"Steinrück","first_name":"Hans-Georg"},{"first_name":"Harald","last_name":"Reichert","full_name":"Reichert, Harald"},{"first_name":"Benjamin M.","last_name":"Ocko","full_name":"Ocko, Benjamin M."},{"full_name":"Deutsch, Moshe","last_name":"Deutsch","first_name":"Moshe"}],"volume":115,"date_updated":"2022-01-06T06:55:57Z","doi":"10.1073/pnas.1716418115","title":"Surface structure evolution in a homologous series of ionic liquids","publication_status":"published","publication_identifier":{"issn":["0027-8424","1091-6490"]},"citation":{"ama":"Haddad J, Pontoni D, Murphy BM, et al. Surface structure evolution in a homologous series of ionic liquids. <i>Proceedings of the National Academy of Sciences</i>. 2018;115:E1100-E1107. doi:<a href=\"https://doi.org/10.1073/pnas.1716418115\">10.1073/pnas.1716418115</a>","chicago":"Haddad, Julia, Diego Pontoni, Bridget M. Murphy, Sven Festersen, Benjamin Runge, Olaf M. Magnussen, Hans-Georg Steinrück, Harald Reichert, Benjamin M. Ocko, and Moshe Deutsch. “Surface Structure Evolution in a Homologous Series of Ionic Liquids.” <i>Proceedings of the National Academy of Sciences</i> 115 (2018): E1100–1107. <a href=\"https://doi.org/10.1073/pnas.1716418115\">https://doi.org/10.1073/pnas.1716418115</a>.","ieee":"J. Haddad <i>et al.</i>, “Surface structure evolution in a homologous series of ionic liquids,” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, pp. E1100–E1107, 2018, doi: <a href=\"https://doi.org/10.1073/pnas.1716418115\">10.1073/pnas.1716418115</a>.","apa":"Haddad, J., Pontoni, D., Murphy, B. M., Festersen, S., Runge, B., Magnussen, O. M., Steinrück, H.-G., Reichert, H., Ocko, B. M., &#38; Deutsch, M. (2018). Surface structure evolution in a homologous series of ionic liquids. <i>Proceedings of the National Academy of Sciences</i>, <i>115</i>, E1100–E1107. <a href=\"https://doi.org/10.1073/pnas.1716418115\">https://doi.org/10.1073/pnas.1716418115</a>","bibtex":"@article{Haddad_Pontoni_Murphy_Festersen_Runge_Magnussen_Steinrück_Reichert_Ocko_Deutsch_2018, title={Surface structure evolution in a homologous series of ionic liquids}, volume={115}, DOI={<a href=\"https://doi.org/10.1073/pnas.1716418115\">10.1073/pnas.1716418115</a>}, journal={Proceedings of the National Academy of Sciences}, author={Haddad, Julia and Pontoni, Diego and Murphy, Bridget M. and Festersen, Sven and Runge, Benjamin and Magnussen, Olaf M. and Steinrück, Hans-Georg and Reichert, Harald and Ocko, Benjamin M. and Deutsch, Moshe}, year={2018}, pages={E1100–E1107} }","short":"J. Haddad, D. Pontoni, B.M. Murphy, S. Festersen, B. Runge, O.M. Magnussen, H.-G. Steinrück, H. Reichert, B.M. Ocko, M. Deutsch, Proceedings of the National Academy of Sciences 115 (2018) E1100–E1107.","mla":"Haddad, Julia, et al. “Surface Structure Evolution in a Homologous Series of Ionic Liquids.” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, 2018, pp. E1100–07, doi:<a href=\"https://doi.org/10.1073/pnas.1716418115\">10.1073/pnas.1716418115</a>."},"intvolume":"       115","page":"E1100-E1107","year":"2018","user_id":"84268","department":[{"_id":"633"}],"_id":"23626","language":[{"iso":"eng"}],"type":"journal_article","publication":"Proceedings of the National Academy of Sciences","status":"public","abstract":[{"lang":"eng","text":"<jats:p>Interfaces of room temperature ionic liquids (RTILs) are important for both applications and basic science and are therefore intensely studied. However, the evolution of their interface structure with the cation’s alkyl chain length n from Coulomb to van der Waals interaction domination has not yet been studied for even a single broad homologous RTIL series. We present here such a study of the liquid–air interface for <jats:inline-formula><m:math xmlns:m=\"http://www.w3.org/1998/Math/MathML\" overflow=\"scroll\"><m:mrow><m:mpadded width=\"+1.7pt\"><m:mi>n</m:mi></m:mpadded><m:mo>=</m:mo><m:mrow><m:mpadded width=\"+1.7pt\"><m:mn>2</m:mn></m:mpadded><m:mtext>to</m:mtext><m:mo> </m:mo><m:mn>22</m:mn></m:mrow></m:mrow></m:math></jats:inline-formula>, using angstrom-resolution X-ray methods. For <jats:inline-formula><m:math xmlns:m=\"http://www.w3.org/1998/Math/MathML\" overflow=\"scroll\"><m:mrow><m:mpadded width=\"+1.7pt\"><m:mi>n</m:mi></m:mpadded><m:mo mathvariant=\"bold\">&lt;</m:mo><m:mn>6</m:mn></m:mrow></m:math></jats:inline-formula>, a typical “simple liquid” monotonic surface-normal electron density profile <jats:inline-formula><m:math xmlns:m=\"http://www.w3.org/1998/Math/MathML\" overflow=\"scroll\"><m:mrow><m:msub><m:mi>ρ</m:mi><m:mi>e</m:mi></m:msub><m:mrow><m:mo stretchy=\"false\">(</m:mo><m:mi>z</m:mi><m:mo stretchy=\"false\">)</m:mo></m:mrow></m:mrow></m:math></jats:inline-formula> is obtained, like those of water and organic solvents. For <jats:inline-formula><m:math xmlns:m=\"http://www.w3.org/1998/Math/MathML\" overflow=\"scroll\"><m:mrow><m:mpadded width=\"+1.7pt\"><m:mi>n</m:mi></m:mpadded><m:mo mathvariant=\"bold\">&gt;</m:mo><m:mn>6</m:mn></m:mrow></m:math></jats:inline-formula>, increasingly more pronounced nanoscale self-segregation of the molecules’ charged moieties and apolar chains yields surface layering with alternating regions of headgroups and chains. The layering decays into the bulk over a few, to a few tens, of nanometers. The layering periods and decay lengths, their linear n dependence, and slopes are discussed within two models, one with partial-chain interdigitation and the other with liquid-like chains. No surface-parallel long-range order is found within the surface layer. For <jats:inline-formula><m:math xmlns:m=\"http://www.w3.org/1998/Math/MathML\" overflow=\"scroll\"><m:mrow><m:mpadded width=\"+1.7pt\"><m:mi>n</m:mi></m:mpadded><m:mo>=</m:mo><m:mn>22</m:mn></m:mrow></m:math></jats:inline-formula>, a different surface phase is observed above melting. Our results also impact general liquid-phase issues like supramolecular self-aggregation and bulk–surface structure relations.</jats:p>"}]},{"type":"journal_article","status":"public","_id":"41838","user_id":"237","department":[{"_id":"314"}],"publication_status":"published","publication_identifier":{"issn":["0027-8424","1091-6490"]},"citation":{"ama":"Lopez CG, Saldanha O, Huber K, Köster S. Lateral association and elongation of vimentin intermediate filament proteins: A time-resolved light-scattering study. <i>Proceedings of the National Academy of Sciences</i>. 2016;113(40):11152-11157. doi:<a href=\"https://doi.org/10.1073/pnas.1606372113\">10.1073/pnas.1606372113</a>","ieee":"C. G. Lopez, O. Saldanha, K. Huber, and S. Köster, “Lateral association and elongation of vimentin intermediate filament proteins: A time-resolved light-scattering study,” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 40, pp. 11152–11157, 2016, doi: <a href=\"https://doi.org/10.1073/pnas.1606372113\">10.1073/pnas.1606372113</a>.","chicago":"Lopez, Carlos G., Oliva Saldanha, Klaus Huber, and Sarah Köster. “Lateral Association and Elongation of Vimentin Intermediate Filament Proteins: A Time-Resolved Light-Scattering Study.” <i>Proceedings of the National Academy of Sciences</i> 113, no. 40 (2016): 11152–57. <a href=\"https://doi.org/10.1073/pnas.1606372113\">https://doi.org/10.1073/pnas.1606372113</a>.","bibtex":"@article{Lopez_Saldanha_Huber_Köster_2016, title={Lateral association and elongation of vimentin intermediate filament proteins: A time-resolved light-scattering study}, volume={113}, DOI={<a href=\"https://doi.org/10.1073/pnas.1606372113\">10.1073/pnas.1606372113</a>}, number={40}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Lopez, Carlos G. and Saldanha, Oliva and Huber, Klaus and Köster, Sarah}, year={2016}, pages={11152–11157} }","mla":"Lopez, Carlos G., et al. “Lateral Association and Elongation of Vimentin Intermediate Filament Proteins: A Time-Resolved Light-Scattering Study.” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 40, Proceedings of the National Academy of Sciences, 2016, pp. 11152–57, doi:<a href=\"https://doi.org/10.1073/pnas.1606372113\">10.1073/pnas.1606372113</a>.","short":"C.G. Lopez, O. Saldanha, K. Huber, S. Köster, Proceedings of the National Academy of Sciences 113 (2016) 11152–11157.","apa":"Lopez, C. G., Saldanha, O., Huber, K., &#38; Köster, S. (2016). Lateral association and elongation of vimentin intermediate filament proteins: A time-resolved light-scattering study. <i>Proceedings of the National Academy of Sciences</i>, <i>113</i>(40), 11152–11157. <a href=\"https://doi.org/10.1073/pnas.1606372113\">https://doi.org/10.1073/pnas.1606372113</a>"},"intvolume":"       113","page":"11152-11157","date_updated":"2023-02-06T12:49:55Z","author":[{"first_name":"Carlos G.","full_name":"Lopez, Carlos G.","last_name":"Lopez"},{"first_name":"Oliva","last_name":"Saldanha","full_name":"Saldanha, Oliva"},{"first_name":"Klaus","last_name":"Huber","full_name":"Huber, Klaus","id":"237"},{"full_name":"Köster, Sarah","last_name":"Köster","first_name":"Sarah"}],"volume":113,"doi":"10.1073/pnas.1606372113","publication":"Proceedings of the National Academy of Sciences","abstract":[{"lang":"eng","text":"<jats:title>Significance</jats:title>\r\n          <jats:p>The hierarchical assembly pathway of the cytoskeletal protein vimentin may be responsible for the astonishing mechanical properties of the emerging filaments, such as high flexibility and extensibility, and thus play a key role in cellular mechanics. A two-step assembly mechanism, involving a lateral and a subsequent elongational step, has been established; however, the elongational step could not be followed in solution. Here, we show direct in situ observation and modeling of the elongation reaction of the filaments on the relevant length and time scales, using time-resolved, multiangle static and dynamic light scattering. We thus achieve sufficient spatio-temporal resolution without the need of labeling, staining, or adsorption to substrates.</jats:p>"}],"keyword":["Multidisciplinary"],"language":[{"iso":"eng"}],"issue":"40","year":"2016","publisher":"Proceedings of the National Academy of Sciences","date_created":"2023-02-06T12:49:36Z","title":"Lateral association and elongation of vimentin intermediate filament proteins: A time-resolved light-scattering study"},{"publication":"Proceedings of the National Academy of Sciences (PNAS)","type":"journal_article","abstract":[{"text":"Optical 2D Fourier transform spectroscopy (2DFTS) provides insight into the many-body interactions in direct gap semiconductors by separating the contributions to the coherent nonlinear optical response. We demonstrate these features of optical 2DFTS by studying the heavy-hole and light-hole excitonic resonances in a gallium arsenide quantum well at low temperature. Varying the polarization of the incident beams exploits selection rules to achieve further separation. Calculations using a full many-body theory agree well with experimental results and unambiguously demonstrate the dominance of many-body physics.","lang":"eng"}],"status":"public","_id":"23487","department":[{"_id":"15"},{"_id":"170"},{"_id":"293"},{"_id":"230"}],"user_id":"49063","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0027-8424","1091-6490"]},"publication_status":"published","issue":"36","year":"2007","page":"14227-14232","intvolume":"       104","citation":{"mla":"Zhang, T., et al. “Polarization-Dependent Optical 2D Fourier Transform Spectroscopy of Semiconductors.” <i>Proceedings of the National Academy of Sciences (PNAS)</i>, vol. 104, no. 36, 2007, pp. 14227–32, doi:<a href=\"https://doi.org/10.1073/pnas.0701273104\">10.1073/pnas.0701273104</a>.","bibtex":"@article{Zhang_Kuznetsova_Meier_Li_Mirin_Thomas_Cundiff_2007, title={Polarization-dependent optical 2D Fourier transform spectroscopy of semiconductors}, volume={104}, DOI={<a href=\"https://doi.org/10.1073/pnas.0701273104\">10.1073/pnas.0701273104</a>}, number={36}, journal={Proceedings of the National Academy of Sciences (PNAS)}, author={Zhang, T. and Kuznetsova, I. and Meier, Torsten and Li, X. and Mirin, R. P. and Thomas, P. and Cundiff, S. T.}, year={2007}, pages={14227–14232} }","short":"T. Zhang, I. Kuznetsova, T. Meier, X. Li, R.P. Mirin, P. Thomas, S.T. Cundiff, Proceedings of the National Academy of Sciences (PNAS) 104 (2007) 14227–14232.","apa":"Zhang, T., Kuznetsova, I., Meier, T., Li, X., Mirin, R. P., Thomas, P., &#38; Cundiff, S. T. (2007). Polarization-dependent optical 2D Fourier transform spectroscopy of semiconductors. <i>Proceedings of the National Academy of Sciences (PNAS)</i>, <i>104</i>(36), 14227–14232. <a href=\"https://doi.org/10.1073/pnas.0701273104\">https://doi.org/10.1073/pnas.0701273104</a>","chicago":"Zhang, T., I. Kuznetsova, Torsten Meier, X. Li, R. P. Mirin, P. Thomas, and S. T. Cundiff. “Polarization-Dependent Optical 2D Fourier Transform Spectroscopy of Semiconductors.” <i>Proceedings of the National Academy of Sciences (PNAS)</i> 104, no. 36 (2007): 14227–32. <a href=\"https://doi.org/10.1073/pnas.0701273104\">https://doi.org/10.1073/pnas.0701273104</a>.","ieee":"T. Zhang <i>et al.</i>, “Polarization-dependent optical 2D Fourier transform spectroscopy of semiconductors,” <i>Proceedings of the National Academy of Sciences (PNAS)</i>, vol. 104, no. 36, pp. 14227–14232, 2007, doi: <a href=\"https://doi.org/10.1073/pnas.0701273104\">10.1073/pnas.0701273104</a>.","ama":"Zhang T, Kuznetsova I, Meier T, et al. Polarization-dependent optical 2D Fourier transform spectroscopy of semiconductors. <i>Proceedings of the National Academy of Sciences (PNAS)</i>. 2007;104(36):14227-14232. doi:<a href=\"https://doi.org/10.1073/pnas.0701273104\">10.1073/pnas.0701273104</a>"},"date_updated":"2023-04-21T22:45:08Z","volume":104,"author":[{"first_name":"T.","last_name":"Zhang","full_name":"Zhang, T."},{"first_name":"I.","full_name":"Kuznetsova, I.","last_name":"Kuznetsova"},{"orcid":"0000-0001-8864-2072","last_name":"Meier","full_name":"Meier, Torsten","id":"344","first_name":"Torsten"},{"last_name":"Li","full_name":"Li, X.","first_name":"X."},{"full_name":"Mirin, R. P.","last_name":"Mirin","first_name":"R. P."},{"full_name":"Thomas, P.","last_name":"Thomas","first_name":"P."},{"full_name":"Cundiff, S. T.","last_name":"Cundiff","first_name":"S. T."}],"date_created":"2021-08-24T09:08:25Z","title":"Polarization-dependent optical 2D Fourier transform spectroscopy of semiconductors","doi":"10.1073/pnas.0701273104"}]